Molecular Basis for poly(A) RNP Architecture and Recognition by the Pan2-Pan3 Deadenylase

The stability of eukaryotic mRNAs is dependent on a ribonucleoprotein (RNP) complex of poly(A)-binding proteins (PABPC1/Pab1) organized on the poly(A) tail. This poly(A) RNP not only protects mRNAs from premature degradation but also stimulates the Pan2-Pan3 deadenylase complex to catalyze the first step of poly(A) tail shortening. We reconstituted this process in vitro using recombinant proteins and show that Pan2-Pan3 associates with and degrades poly(A) RNPs containing two or more Pab1 molecules. The cryo-EM structure of Pan2-Pan3 in complex with a poly(A) RNP composed of 90 adenosines and three Pab1 protomers shows how the oligomerization interfaces of Pab1 are recognized by conserved features of the deadenylase and thread the poly(A) RNA substrate into the nuclease active site. The structure reveals the basis for the periodic repeating architecture at the 3' end of cytoplasmic mRNAs. This illustrates mechanistically how RNA-bound Pab1 oligomers act as rulers for poly(A) tail length over the mRNAs' lifetime.We would like to thank ... the MPIB cryo-EM, and core facilities ..

A construction of Frobenius manifolds with logarithmic poles and applications

A construction theorem for Frobenius manifolds with logarithmic poles is established. This is a generalization of a theorem of Hertling and Manin. As an application we prove a generalization of the reconstruction theorem of Kontsevich and Manin for projective smooth varieties with convergent Gromov-Witten potential. A second application is a construction of Frobenius manifolds out of a variation of polarized Hodge structures which degenerates along a normal crossing divisor when certain generation conditions are fulfilled.Comment: 46 page

Elliptical dichroism: operating principle of planar chiral metamaterials

We employ a homogenization technique based on the Lorentz electronic theory to show that planar chiral structures (PCSs) can be described by an effective dielectric tensor similar to that of biaxial elliptically dichroic crystals. Such a crystal is shown to behave like a PCS insofar as it exhibits its characteristic optical properties, namely, co-rotating elliptical polarization eigenstates and asymmetric, direction-dependent transmission for left/right-handed incident wave polarization.Comment: 3 pages, version as accepted in Optics Letters but before final shortening

BMPix and PEAK tools: New methods for automated laminae recognition and counting — Application to glacial varves from Antarctic marine sediment

We present tools for rapid and quantitative detection of sediment lamination. The BMPix tool extracts color and gray-scale curves from images at pixel resolution. The PEAK tool uses the gray-scale curve and performs, for the first time, fully automated counting of laminae based on three methods. The maximum count algorithm counts every bright peak of a couplet of two laminae (annual resolution) in a smoothed curve. The zero-crossing algorithm counts every positive and negative halfway-passage of the curve through a wide moving average, separating the record into bright and dark intervals (seasonal resolution). The same is true for the frequency truncation method, which uses Fourier transformation to decompose the curve into its frequency components before counting positive and negative passages. We applied the new methods successfully to tree rings, to well-dated and already manually counted marine varves from Saanich Inlet, and to marine laminae from the Antarctic continental margin. In combination with AMS14C dating, we found convincing evidence that laminations in Weddell Sea sites represent varves, deposited continuously over several millennia during the last glacial maximum. The new tools offer several advantages over previous methods. The counting procedures are based on a moving average generated from gray-scale curves instead of manual counting. Hence, results are highly objective and rely on reproducible mathematical criteria. Also, the PEAK tool measures the thickness of each year or season. Since all information required is displayed graphically, interactive optimization of the counting algorithms can be achieved quickly and conveniently